The structure is the message: Preserving experimental context through tensor decomposition

Tan, Zhixin Cyrillus; Meyer, Aaron S.

doi:10.1016/j.cels.2024.07.004

Cell Systems

2024

DOI: 10.1016/j.cels.2024.07.004

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The structure is the message: Preserving experimental context through tensor decomposition

Zhixin Cyrillus Tan,

Aaron S. Meyer

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Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood

Orcutt-Jahns,

Lima Junior,

Lin

et al. 2024

npj Syst Biol Appl

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Cytokines operate in concert to maintain immune homeostasis and coordinate immune responses. In cases of ER+ breast cancer, peripheral immune cells exhibit altered responses to several cytokines, and these alterations are correlated strongly with patient outcomes. To develop a systems-level understanding of this dysregulation, we measured a panel of cytokine responses and receptor abundances in the peripheral blood of healthy controls and ER+ breast cancer patients across immune cell types. Using tensor factorization to model this multidimensional data, we found that breast cancer patients exhibited widespread alterations in response, including drastically reduced response to IL-10 and heightened basal levels of pSmad2/3 and pSTAT4. ER+ patients also featured upregulation of PD-L1, IL6Rα, and IL2Rα, among other receptors. Despite this, alterations in response to cytokines were not explained by changes in receptor abundances. Thus, tensor factorization helped to reveal a coordinated reprogramming of the immune system that was consistent across our cohort.

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Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood

Orcutt-Jahns,

Lima Junior,

Lin

et al. 2024

npj Syst Biol Appl

View full text Add to dashboard Cite

show abstract

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The structure is the message: Preserving experimental context through tensor decomposition

Cited by 1 publication

References 50 publications

Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood

Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood

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